Bede Constantinides

186 Followers
280 Following
31 Posts
Interested in pathogen evolution and scalable genomics. Researcher at the University of Birmingham
Bloghttps://bede.im

Some hard truths for open source adoption from @bert_hubert

His #1 is also my #1:

"Whatever you’re building, you have NO margin to get away with being uglier/harder/more difficult than big tech"

and "If you don’t have people who deeply care about user-experience in your team, you’re doomed"

Open source has so many adoption barriers that only people who care a LOT will get over them. But honestly, most people don't have enough care to spare right now.

Worth a read.

https://berthub.eu/articles/posts/what-the-open-world-must-do-better/

What we in the open world are messing up in trying to compete with big tech - Bert Hubert's writings

Our societies and governments now largely run on American proprietary big-tech platforms. Many of us want to decrease this dependency, or even end it altogether. This article is part of a series of posts on (European) cloud challenges. Everyone in the open tech scene is full of good intentions and we all want to improve things, but mostly we are not succeeding. By our nature, we would like to build fun, open, federated, and standards-based things.

Bert Hubert's writings
Bioinformaticians are impatient👇
Conda is notorious slow... then I found mamba https://github.com/mamba-org/mamba, then I found
pixi https://prefix.dev/blog/pixi_a_fast_conda_alternative : Blazing fast cross-platform package management for teams.
By the creators of the mamba package manager. #bioinformatics
GitHub - mamba-org/mamba: The Fast Cross-Platform Package Manager

The Fast Cross-Platform Package Manager. Contribute to mamba-org/mamba development by creating an account on GitHub.

GitHub
Hostile 1.0.0 released and live on Bioconda
- Adds human genomes masked against bacteria, viruses and phage
- Improved automatic index download
- Improved genome masking
- Bug fixes
https://github.com/bede/hostile
GitHub - bede/hostile: Accurate host read removal

Accurate host read removal. Contribute to bede/hostile development by creating an account on GitHub.

GitHub
Clear Aeropress confirms long-held hypothesis that even the most gentle swirling after inversion (to remove stuck grounds on plunger) creates a problematic domed coffee bed

After positive reviews, the paper about our host decontamination approach 'Hostile' was accepted in Oxford Bioinformatics:
https://doi.org/10.1093/bioinformatics/btad728

Related blog post:
https://log.bede.im/2023/08/29/precise-host-read-removal.html

Hostile: accurate decontamination of microbial host sequences

AbstractMotivation. Microbial sequences generated from clinical samples are often contaminated with human host sequences that must be removed for ethical and le

OUP Academic
Simple utility for making robust sequence checksums from one or many FASTA/Q records
https://github.com/bede/seqsum
GitHub - bede/seqsum: Robust individual and aggregate checksums for nucleotide sequences

Robust individual and aggregate checksums for nucleotide sequences - GitHub - bede/seqsum: Robust individual and aggregate checksums for nucleotide sequences

GitHub
Just published in JOSS: 'gesel: a JavaScript package for client-side gene set enrichment' https://doi.org/10.21105/joss.05777
gesel: a JavaScript package for client-side gene set enrichment

Lun et al., (2023). gesel: a JavaScript package for client-side gene set enrichment. Journal of Open Source Software, 8(90), 5777, https://doi.org/10.21105/joss.05777

Journal of Open Source Software
We've made it even easier to discover new viruses! Consensus genomes are now part of the standard output for the Twist Comprehensive and Respiratory Viral Research analyses. Find out more in our blog post: https://www.onecodex.com/blog/2023/08/22/consensus-genomes-using-twist-research-panels/
One Codex automatically generates consensus sequences from Twist Viral Research Panels

One Codex now automatically generates consensus genome sequences for the Twist Viral Research Panels

Blog post: precise removal of host DNA sequences https://log.bede.im/2023/08/29/precise-host-read-removal.html

On that story about scientists leaving X and coming here. Please, please lean into the feature of hashtag following and tag your stuff. A lot of us would love to find you and hashtag discovery is the easiest way here.

#scientists #scientist #mastodon #followers #discovery #news #science